Slicer instructions - incomplete?

[mathieuboudreau]

b0-fieldmap-realistic-simulation/smoothing_procedure.py

Lines 25 to 30 in f166ff5

	Example to run the script in a terminal:
	Slicer.exe --python-script smoothing_procedure.py
	-m "C:/path/to/main_volume.nii.gz"
	-s "C:/path/to/segmentation.nii.gz"
	-o "C:/path/to/output_labelmap.nii.gz"

Hi @CharlesPageot - I installed Slicer and am trying to replicate your smoothed skulls, however the instructions in these files are not working for me. Am I missing additional setup steps to run your script?

(base) mathieuboudreau@Mathieus-MacBook-Pro b0-fieldmap-realistic-simulation %  /Applications/Slicer.app/Contents/MacOS/Slicer --python-script smoothing_procedure.py -m data/sub-amuAL_T1w.nii.gz -s data/sub-amuAL_T1w_label-brain_dseg.nii.gz -o data/slicer_smoothing_output.nii.gz
Error #1 while writing setting "Modules/AdditionalPaths"
Error #1 while writing setting "Modules/IgnoreModules"
Error #1 while writing setting "Extensions/ManagerEnabled"
Error #1 while writing setting "Extensions/ServerUrl"
Error #1 while writing setting "Extensions/FrontendServerUrl"
Error #1 while writing setting "Extensions/InstallPath"
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
Switch to module:  "Welcome"
Populating font family aliases took 73 ms. Replace uses of missing font family ".AppleSystemUIFont" with one that exists to avoid this cost. 
Traceback (most recent call last):
  File "<string>", line 5, in <module>
  File "<string>", line 3, in <module>
ModuleNotFoundError: No module named 'click'
Switch to module:  ""
Switch to module:  ""

click was installed locally through pipy in my base, but maybe Slicer doesn't see that path

[CharlesPageot]

Yeah it looks like Slicer doesn't see it. Maybe if you try to install click inside Slicer's embedded Python environment?